BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy2966
         (237 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 93/221 (42%), Gaps = 37/221 (16%)

Query: 5   CAQDTLPTLAQAIFFCGAIVGGLVFGWVADHFGRIPALVGTNLTGFVAGVATA------- 57
            A ++L     A    G I+GG + G+ ++ FGR  +L    +  F++GV +A       
Sbjct: 51  SAANSLLGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFT 110

Query: 58  -----------FASTFWQFAICRFF--VGLAFDNCFTMMYILVLEYVGPSWRTFVANMSI 104
                       A    +F I R    +G+   +  + MYI  L       +    N   
Sbjct: 111 SINPDNTVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFA 170

Query: 105 AIFFTLAASLLPWIAYYVA-----------NWQYLCVITSLPLLVAVITPWIVPESARWL 153
            IF  L   L+  + Y++A            W+Y+     +P L+ ++  + VPES RWL
Sbjct: 171 IIFGQL---LVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWL 227

Query: 154 VSQGRVDEAVVIMKRFEKINNKKVDPKLYQQLKETCQRQAK 194
           +S+G+ ++A  I++   KI    +  +  Q++K +     K
Sbjct: 228 MSRGKQEQAEGILR---KIMGNTLATQAVQEIKHSLDHGRK 265


>pdb|2HYE|C Chain C, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
          Length = 759

 Score = 29.6 bits (65), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/37 (35%), Positives = 21/37 (56%)

Query: 170 EKINNKKVDPKLYQQLKETCQRQAKQEIDGKRYSVLD 206
           E + + KV P LY+QL++ C+   + +I   R   LD
Sbjct: 91  ENLCSHKVSPMLYKQLRQACEDHVQAQILPFREDSLD 127


>pdb|4A0K|A Chain A, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
           Site Containing Dna-Duplex
          Length = 742

 Score = 29.6 bits (65), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/37 (35%), Positives = 21/37 (56%)

Query: 170 EKINNKKVDPKLYQQLKETCQRQAKQEIDGKRYSVLD 206
           E + + KV P LY+QL++ C+   + +I   R   LD
Sbjct: 74  ENLCSHKVSPMLYKQLRQACEDHVQAQILPFREDSLD 110


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.331    0.142    0.467 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,661,848
Number of Sequences: 62578
Number of extensions: 242538
Number of successful extensions: 682
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 678
Number of HSP's gapped (non-prelim): 4
length of query: 237
length of database: 14,973,337
effective HSP length: 96
effective length of query: 141
effective length of database: 8,965,849
effective search space: 1264184709
effective search space used: 1264184709
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 bits)